Commit c9a9d48a authored by Thomas Vincent's avatar Thomas Vincent

rework intensity view page

parent 4e940794
.. _intensity_view:
Converting to Q-Space (Intensity view)
======================================
Intensity View
==============
.. |intensity_view| image:: img/intensity_view.png
.. |draw_roi_button| image:: img/draw_roi_button.png
.. |to_qspace_button| image:: img/to_qspace_button.png
.. figure:: img/intensity_view.png
:width: 100%
:align: center
+------------------+
| Intensity view |
+==================+
| |intensity_view| |
+------------------+
Intensity view
This view display the total acquired intensity over the sample.
When an entry is selected in the list on the left, each point on the scatter
plot represents the total intensity of the acquired image at that point.
By default, this view displays the total intensity summed over all scans for each point of the sample.
When the root node (labeled ``Intensity``) is selected, the total intensity of
all entries is displayed.
Select displayed data
---------------------
The list on the left allows you to select the entries that will be used when
converting to q-space.
When an entry is selected in the list on the left, the scatter plot represents the intensity of the acquired images for the selected entry.
When the **Total** item is selected, the total intensity of selected entries is displayed.
You can select points on the central scatter plot to display an intensity
profile at that point at the bottom of the window.
It is possible to change the sorting of the scans by changing the selected positioner in the **Sort by** drop-down list (`eta` by default).
Roi selection
.............
It is possible to normalize the displayed data with the **Normalization** drop-down list.
Before starting the conversion, a ROI (Region Of Interest) must be selected
on the scatter plot. To draw a ROI, click on the |draw_roi_button| icon on the
right and then select an area on the scatter plot.
By clicking on a point of the scatter plot, you can display an intensity profile at that point in the lower part of the window.
When this is done, click on the |to_qspace_button| to open the :ref:`conversion window <conversion_window>`.
Shift scan sample positions
---------------------------
Conversion parameters
.....................
TODO
Please see the :ref:`conversion window <conversion_window>` documentation.
Prepare Q space conversion
--------------------------
When the conversion is done, a new :ref:`qspace item <qspace_item>` is
added to the :ref:`project tree <project_tree>`. You can view the result in
the :ref:`qspace view <qspace_view>`.
Click on the |to_qspace_button| button in the **ROI** panel on the right side of the window to start a Q space conversion of all sample points.
This opens the :ref:`QSpace conversion dialog <conversion_window>`.
Select scans
............
To run a Q space conversion for a subset of the scans, select only the one that you want to use in the list on the left side of the window.
Sample ROI selection
....................
You can select a rectangular ROI to select the sample positions for which you want to run a QSpace conversion.
To draw a ROI, click on the |draw_roi_button| button in the right panel and then draw the selected area on the scatter plot.
Once this is done, click on the |to_qspace_button| button to open the :ref:`QSpace conversion dialog <conversion_window>`.
......@@ -171,7 +171,7 @@ This can take quite some time depending on the size of the acquired data.
Open project summary page
Finally, the project summary page (:numref:`figure_open_dialog`) provides the description of the scans from which the project has been created.
Click on **Finish** to display the newly created project in the :ref:`project tree window <project_tree>`.
Click on **Finish** to display the newly created project in the :ref:`project tree window <project_tree>` and the :ref:`intensity view <intensity_view>`.
.. _load_project:
......@@ -186,4 +186,4 @@ This opens a file dialog which allows you to browse to and select a ``xsocs.prj`
Once the project file is selected, the project summary page (:numref:`figure_open_dialog`) provides the description of the scans contained in the project.
From there you can either cancel, or click on **Finish** to load the selected project in the :ref:`project tree window <project_tree>`.
From there you can either cancel, or click on **Finish** to load the selected project in the :ref:`project tree window <project_tree>` and the :ref:`intensity view <intensity_view>`.
......@@ -15,10 +15,6 @@ How to use *X-SOCS* to reduce KMAP data, step by step.
usage/project.rst
usage/project_view.rst
usage/intensity_view.rst
usage/conversion.rst
usage/qspace_view.rst
usage/results_view.rst
.. toctree::
:hidden:
usage/conversion.rst
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